Job ID = 8184546 SRX = SRX8047604 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:25:20 prefetch.2.10.7: 1) Downloading 'SRR11471328'... 2020-08-10T04:25:20 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:27:09 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:27:09 prefetch.2.10.7: 1) 'SRR11471328' was downloaded successfully Read 17808165 spots for SRR11471328/SRR11471328.sra Written 17808165 spots for SRR11471328/SRR11471328.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:13 17808165 reads; of these: 17808165 (100.00%) were unpaired; of these: 2189683 (12.30%) aligned 0 times 11694148 (65.67%) aligned exactly 1 time 3924334 (22.04%) aligned >1 times 87.70% overall alignment rate Time searching: 00:21:18 Overall time: 00:21:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9074968 / 15618482 = 0.5810 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 13:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 10 Aug 2020 13:53:48: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:53:48: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:53:55: 1000000 INFO @ Mon, 10 Aug 2020 13:54:02: 2000000 INFO @ Mon, 10 Aug 2020 13:54:09: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 13:54:16: 4000000 INFO @ Mon, 10 Aug 2020 13:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 10 Aug 2020 13:54:18: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:54:18: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:54:25: 5000000 INFO @ Mon, 10 Aug 2020 13:54:26: 1000000 INFO @ Mon, 10 Aug 2020 13:54:33: 6000000 INFO @ Mon, 10 Aug 2020 13:54:35: 2000000 INFO @ Mon, 10 Aug 2020 13:54:38: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:54:38: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:54:38: #1 total tags in treatment: 6543514 INFO @ Mon, 10 Aug 2020 13:54:38: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:54:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:54:38: #1 tags after filtering in treatment: 6543323 INFO @ Mon, 10 Aug 2020 13:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:54:38: #1 finished! INFO @ Mon, 10 Aug 2020 13:54:38: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:54:40: #2 number of paired peaks: 29972 INFO @ Mon, 10 Aug 2020 13:54:40: start model_add_line... INFO @ Mon, 10 Aug 2020 13:54:40: start X-correlation... INFO @ Mon, 10 Aug 2020 13:54:40: end of X-cor INFO @ Mon, 10 Aug 2020 13:54:40: #2 finished! INFO @ Mon, 10 Aug 2020 13:54:40: #2 predicted fragment length is 97 bps INFO @ Mon, 10 Aug 2020 13:54:40: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 10 Aug 2020 13:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05_model.r WARNING @ Mon, 10 Aug 2020 13:54:40: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:54:40: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 10 Aug 2020 13:54:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:54:40: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:54:44: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 13:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 10 Aug 2020 13:54:48: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:54:48: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:54:52: 4000000 INFO @ Mon, 10 Aug 2020 13:54:57: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:54:58: 1000000 INFO @ Mon, 10 Aug 2020 13:55:01: 5000000 INFO @ Mon, 10 Aug 2020 13:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.05_summits.bed INFO @ Mon, 10 Aug 2020 13:55:06: Done! INFO @ Mon, 10 Aug 2020 13:55:07: 2000000 pass1 - making usageList (82 chroms): 8 millis pass2 - checking and writing primary data (2260 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:55:10: 6000000 INFO @ Mon, 10 Aug 2020 13:55:15: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:55:15: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:55:15: #1 total tags in treatment: 6543514 INFO @ Mon, 10 Aug 2020 13:55:15: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:55:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:55:15: #1 tags after filtering in treatment: 6543323 INFO @ Mon, 10 Aug 2020 13:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:55:15: #1 finished! INFO @ Mon, 10 Aug 2020 13:55:15: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:55:15: 3000000 INFO @ Mon, 10 Aug 2020 13:55:17: #2 number of paired peaks: 29972 INFO @ Mon, 10 Aug 2020 13:55:17: start model_add_line... INFO @ Mon, 10 Aug 2020 13:55:17: start X-correlation... INFO @ Mon, 10 Aug 2020 13:55:17: end of X-cor INFO @ Mon, 10 Aug 2020 13:55:17: #2 finished! INFO @ Mon, 10 Aug 2020 13:55:17: #2 predicted fragment length is 97 bps INFO @ Mon, 10 Aug 2020 13:55:17: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 10 Aug 2020 13:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10_model.r WARNING @ Mon, 10 Aug 2020 13:55:17: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:55:17: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 10 Aug 2020 13:55:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:55:17: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:55:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:55:24: 4000000 INFO @ Mon, 10 Aug 2020 13:55:32: 5000000 INFO @ Mon, 10 Aug 2020 13:55:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:55:41: 6000000 INFO @ Mon, 10 Aug 2020 13:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.10_summits.bed INFO @ Mon, 10 Aug 2020 13:55:43: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (735 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:55:45: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:55:45: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:55:45: #1 total tags in treatment: 6543514 INFO @ Mon, 10 Aug 2020 13:55:45: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:55:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:55:45: #1 tags after filtering in treatment: 6543323 INFO @ Mon, 10 Aug 2020 13:55:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:55:45: #1 finished! INFO @ Mon, 10 Aug 2020 13:55:45: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:55:47: #2 number of paired peaks: 29972 INFO @ Mon, 10 Aug 2020 13:55:47: start model_add_line... INFO @ Mon, 10 Aug 2020 13:55:47: start X-correlation... INFO @ Mon, 10 Aug 2020 13:55:47: end of X-cor INFO @ Mon, 10 Aug 2020 13:55:47: #2 finished! INFO @ Mon, 10 Aug 2020 13:55:47: #2 predicted fragment length is 97 bps INFO @ Mon, 10 Aug 2020 13:55:47: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 10 Aug 2020 13:55:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20_model.r WARNING @ Mon, 10 Aug 2020 13:55:48: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:55:48: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 10 Aug 2020 13:55:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:55:48: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:55:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:56:04: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047604/SRX8047604.20_summits.bed INFO @ Mon, 10 Aug 2020 13:56:13: Done! pass1 - making usageList (37 chroms): 3 millis pass2 - checking and writing primary data (248 records, 4 fields): 10 millis CompletedMACS2peakCalling